fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-09-29 09:58:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

r421: removed the MM_F_SPLICE_BOTH mode

Browse Source 
In the default splice mode, minimap2 applies two rounds of spliced alignment:
first assuming GT-AG to be the splice signal across all splicing sites and then
assuming CT-AC to be the signal. This is the idea strategy.

In the MM_F_SPLICE_BOTH mode, minimap2 applies one round of spliced alignment,
assuming GT-AG and CT-AC to be the splice signals AT THE SAME TIME. This will
be faster but less accurate. I don't think anyone would like to run minimap2 in
this mode, so I am removing it for clarity.
This commit is contained in:
Heng Li
2017-09-20 11:11:53 -04:00
parent a686461e83
commit 75e6bbc9f6
4 changed files with 14 additions and 21 deletions
Download Patch File Download Diff File Expand all files Collapse all files
map.c
+2 -2
View File
@@ -38,8 +38,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
{
if (opt->flag & MM_F_SPLICE_BOTH)
opt->flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV);
if ((opt->flag & MM_F_SPLICE_FOR) && (opt->flag & MM_F_SPLICE_REV))
opt->flag |= MM_F_SPLICE;
if (opt->mid_occ <= 0)
opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac);
if (mm_verbose >= 3)